The missing scenes
by AltanKatt
Summary: This will be a collection of scenes I would like to have seen in the series. Meetings, transitions, conversations we never saw. This was my first fan fiction Writing and I move the scenes from here to the novel as I reach the Point in the story where it fits. Let me know if you want me to fill a gap in the story.
1. Neal is going back to prison, end of S1

_This scene takes place after the ending of season 1._

* * *

The chaos had begun to settle. The burning plane was a pile of smoldering black leftovers. Peter did not want to think about the bodies in there somewhere. The pilots and Kate. He turned towards the office where he had seen the crises-person take Neal. The blinders were still down. He wished he could be there for Neal, but he had to face his own shock before he could handle others'. A professional, trained to take care of people in these situations was the best he could offer Neal right now. Another had talked to him for an hour while they put the fire out. But it was not his girlfriend who had been blown to pieces and his future that gone up in smoke.

Hughes turned up by his side.

"How are you, Peter?"

"I can manage."

"And Caffrey?" Peter nodded towards the office.

"Probably not as well."

"Peter, the Marshals are here to bring him back to prison."

"What?!" Hughes gave him a look as if he should have seen this coming. Peter took a deep breath and saw the situation from another point of view.

"Hughes, he wasn't running."

"Perhaps. And he may not have anything to do with the bomb on that plane either. But until we know…"

"We have to see him as a fleeing felon and a murder suspect," Peter finished with a sigh. Hughes nodded. It made sense. And yet not. Because he knew Neal and knew about the deal with Fowler. But he did not know Fowler and if he had fooled Neal or not. Or if Fowler, in turn, had been set up by someone else.

"As soon as he's ready for it, I'll take him back" Peter assured his boss, who shook his head.

"I'm sorry, Peter, but you're still under suspension, and in either case is Neal an inmate on a maximum security prison. You know what that means." Peter watched the group of marshals waiting. One of them held a set of cuffs and chains meant for transports of high-security felons.

"Reese…" Peter began, searching for words for a protest he knew would be in vain. He would not even need to put ordinary handcuffs on Neal. No one would need more than that as long as they treated him fair.

"They're not animals, Peter. They'll wait until he's ready to leave that room on his own two feet. But Peter, he needs to be told."

Peter nodded.

"I'll tell him." Had it been anyone but Neal, maybe he had been considered cruel by taking this task upon himself. Especially when he was not there to comfort him in his grief. Neal, however, had always respected his role as an FBI agent and been able to combine this with friendship. He figured Neal had succeeded better in this than Peter himself.

He walked to the office and knocked on the door. A woman's soft voice from within the room, and then the door opened just enough to face the crisis-person and keep Neal out of sight.

"How is he?"

She had seen them together, Peter keeping Neal from trying to save Kate, so she knew who he was.

"These things take time."

"I know. Can I see him?"

She frowned.

"It's okay Erica, let him in" he heard Neal's voice from inside the room, and she stepped aside. Peter slipped by her, and Erica closed the door behind him. Neal sat on the floor like a wet rag. His face was red and swollen from crying.

"Hi, Peter."

"Hi, Neal."

Peter turned to Erica.

"Can you leave us alone, please?"

Erica checked with Neal, who nodded.

"I'll be nearby if you need me."

Peter leaned against a desk, unwilling to make himself comfortable in the room. He felt Neal's eyes upon him and he realized he avoided to face him. He turned his head and met Neal's gaze.

"What aren't you telling me, Peter?" Observant as always.

"I wish this could be done differently" Peter started. "And I know, you would come with me if I told you to. But as it is, I don't have a badge."

"I'm going back to prison, aren't I?"

"While all this is investigated, yes. I'm sorry, Neal."

The kid nodded.

"They're waiting for me outside?"

"They are." Peter's eyes wandered away. "Neal... " He forced himself to meet the kid's eyes. "You're considered a high-risk transport."

"Leg-irons and black-box, I know the drill, Peter."

Neal's assurance sent a shiver through Peter. He had always seen them as something needed in extreme cases for violent people. Neal had faced them as standard procedure in prison without being violent.

"You can stay in here as long as you need to. If you want to talk some more with Erica, it's fine too. There's no one out there who wishes to drag you out of here in chains until you're capable of handling it."

"Could you put them on me?" Peter stared. "Please?" What was it with this guy?

"Why?"

"I'll be having them on for quite a while before I'm back in prison. Believe it or not, but those things aren't very comfortable in the first place. I know you wouldn't pull them tighter than need."

Peter sighed. Putting him in restraints of that kind was nothing he wanted to at any time but Neal would be far more uncomfortable than him, no matter who put them on.

"Alright, I'll talk to them, see what I can do. But it's not my call."

Neal nodded and got to his feet.

"I'm ready." Neal looked far from ready but there was little Peter could do about it.

"Are you sure?"

"A distraction would suit me fine right now. This will at least be familiar grounds. Yes, Peter, I'm ready." He even sent Peter an assuring smile.

"There's a bathroom in there if you want to freshen up."

Neal left the door open while he washed his face. He closed the door without locking while he did what he needed to do otherwise. Peter heard the toilet flush and Neal appeared in the door.

"Go ahead, Peter."

Peter returned out to the hangar and met the marshals right outside.

"He'll follow with you now, but he has one request."

"Which is?" asked the man Peter figured was the leader of the group.

"That I pat him down and put those restraints on."

The man's eyebrows went up in surprise.

"I've no problem with that, but you're a civilian at the moment, Agent Burke. I'll have to supervise it."

Peter nodded. He was not going to argue against it.

They walked inside the office, the marshal with a handful of chains in his hand. Neal stood as a composed wreck, leaning against a desk, exposed and harmless.

"Neal Caffrey, I'm U.S. Marshal Sam North. I'm going to supervise your transport back to Sing Sing. Agent Burke here tells me you want him to restrain you. Is that correct?"

Neal nodded. The marshal explained to Neal why he had to remain in the room. Neal nodded again and rose from the desk with a blank face, turned his back to them, and held out his arms.

Peter started with Neal's hair, dusty from the explosion. The collar, the sleeves. Peter did not expect to find anything, but he did it correctly. Neal did not expect him to do anything less.

The marshal handed him the restrains. Neal continued to hold his arms out until Peter had locked the belly-chain around his waist. The cuffs around the ankles were not uncomfortable in themselves at least. It was the chain that restricted the length of the step that constituted the restraint. Peter rose to lock the final cuffs around his friend's wrists. No matter how correct he was with this, it would be unpleasant for Neal.

Neal already stood with his hands in position. The cuffs were directly linked to the belly-chain which forced the hands and arms in a fixed position which in the long run could become painful. The black box on top of that removed every option to move the hands. Neal had not flinched once. Not even when Peter put that box on top of it all.

Peter remembered when he had cuffed Neal in the interview room for the transport to the detonation center four and a half years ago. Neal had tried not to flinch when the cuffs closed around his wrists. Peter had cuffed him front with ordinary cuffs. More of a psychological restraint. What he put on Neal now was the opposite, and his CI had not moved a muscle in his face. Prison-time had made its mark, and Peter was not sure if that system created better citizens. It felt healthier to flinch than be used to leg-irons and black boxes.

Neal was restrained, and there was nothing more for Peter to do. Still with his back to the marshal Neal blank face turned to one in grief.

"See you, Peter?"

A question? Did he have to ask?

"Any time, kiddo" he assured Neal. "And I'll do my best to get you out as soon as I can, alright."

Neal nodded.

"Ready to go?" the marshal asked. Peter watched Neal's face transform into one of smiles and playfulness. An imitation of his normal state. Neal turned to face the marshal.

"Can't wait" he replied with a grin.

Peter stepped aside, and the marshal took over. With a grip around Neal's upper arm, he led him out of the office in the pace the chains allowed.


	2. Peter and June talk, end of S1

_This scene is from the end of season 1 after Neal has been brought back to prison (another scene I wrote)_

* * *

Peter walked around in Neal's empty apartment without an actual aim. He just wanted to understand, to make things make sense. Neal had been about to leave, and all he brought was one bag with nothing more than a passport, some cash and a minimal amount of clothes.

Was that the way he had been living before he got arrested? A life with no ties, always ready to leave. In Peter's world that was not a healthy life. A good life was a settled one. It did not seem as that was what Neal wanted. Or did he want it on his own terms? Had Peter pushed him into a situation where he felt he needed to escape?

Now Neal was in prison, and Kate was dead. Nothing had turned out as any of them hoped.

June stood in the open doorway.

"I thought I heard someone moving upstairs."

"I'm sorry." Peter forced to keep his face from reddening. "I just…" He did not find the words to describe what he was doing there.

"You're Neal's handler" June replied with a crisp edge. "You have the right to search his home."

"That's not why I came. I just wanted to understand what was going on in his head. June, Neal is back in prison."

June's stoic pose sank. She pulled out a chair and sat down.

"Oh, Neal. What did he do?"

"Nothing, as far as I know," Peter admitted, feeling guilty, being a part of the system that forced Neal back.

"Then you didn't put him there?"

"It was not my call." He sighed. "Neal was about to leave with Kate after a deal with a guy on OPR. It was all legal. Then the plane exploded on the ground, with Kate inside. Neal was there. And no one understands what happened."

"Neal would never kill Kate" June protested.

"No. He wouldn't."

"And you said it was legal for him to leave?"

"Yes. I did some research to check what he was doing. It was all legal." 'Was' Peter thought. He had seen it. Neal had had an official release from his sentence and had been a free man. Bought with a bribe consisting of a music box, but that was beside the point.

"Then why is he in prison? Because of the explosion?"

"That's one reason. The other is that his deal has vanished. For everyone else, it looks like Neal was about to escape. And that alone is a valid reason to put him back."

"Can you get him out again?"

"I don't know" Peter admitted. "I still haven't got my badge back. I probably will get it back, but…"

"You're not sure if you want Neal back out?"

"No, I do. I do. He is a valuable asset. And a friend. I just… I can't figure out if I'm doing him a favor or not. June, he left all this. For a dream. For a woman he didn't actually know. A woman that hide from him." Peter had never liked Kate. She had never made the impression to care for anyone but herself. "Before I arrested him the first time, he left for Europe without Kate. We kept eyes on Kate with the hope to catch Neal. When he got back, he didn't come near her. Do you know why? Because she was hiding from him. And not once have I heard him question why she did that. Because Neal sees what he wants to see."

"Or he sees the good in people" June pointed out. Peter nodded. Perhaps. Or Neal was just plain naïve when it came to women, and Kate in particular. "But why do you think Neal would do better in prison?" June persisted. Peter sighed, searching for words.

"I wonder how much my behavior caused him to feel he had to leave. When he has served his time, he is free. Free from me. Free to make his own choices. If he's in prison, I can't…" Peter did not want to see Neal in prison, but this was not about what he wanted but what would be best for Neal. And he wanted June to understand that. "He once expressively said he didn't want the life I offered. Maybe I made him feel trapped, instead of helped."

And a trapped Neal is a Neal that runs. And a Neal that escapes his sentence ends up in prison for good. That was the last thing Peter wanted.

He had been walking back and forth. Now he pulled out a chair and sat down, facing June.

"Since he started working for me, I've cuffed him twice without him being guilty of anything. He's a con-man. And to con a con-man so he becomes a prime suspect… He gets the blame for things he didn't do. And he gets the blame just because he works for the FBI, for me. We keep him under a Close watch which seems to make it twice as fun to frame him. He's Neal Caffrey, the greatest con-man ever lived. A challenge for the whole con-man-world out there. And I put him in a position where he cannot defend himself."

"But you proved him innocent the first time" June pointed out. "And I'm sure you can prove him innocent this time too. And that I think is most important; to prove he is innocent when he is. To fight for him. To show him that you're there for him, that you have faith in him."

Peter nodded. It would not be the last time Neal ended up as a suspect. And Neal could use the situation to commit his own crimes and claim he was framed. Peter could not trust him not to. How many times would he hurt Neal by not trusting him when Neal in return trusted him completely? But he did trust Neal, in a peculiar way. Not as unconditional as Neal probably trusted him, but he did trust him with his life and the work he was doing for the FBI. And he had faith in the kid.

"Your husband…" he began, looking at June. "Did he ever…stop?"

"And became an honest citizen?" June clarified the question. Peter nodded. "Yes, he did. For most the part at least."

"What made him quit?"

"Something you cannot control." June smiled. "Kids. A desire to be with them when they grew up and not meet them in an orange jumpsuit on the other side of a glass wall."

Through Peter's mind rushed images of single women he could introduce in Neal's life. He dismissed the idea at once. Neal had to figure things out himself, make his own choices. All Peter could do was to show him what life could be like, give him reasons to stay, and show that he had faith in Neal and would be there for him.


	3. Scene following Checkmate, S3

_This scene is a longer version of the scene ending Checkmate, season 3, where Neal learns that he can be free in three months. By request._

* * *

"What does that mean?" Neal's head was too tumbled over this morning's events to get the juridical mumbo-jumbo to something he could grasp.

"It means no anklet. No nothing. In three months, you could be a free man." Peter was just as stunned as he, it seemed.

Neal grabbed for a chair. He sank down and rested his head in his hands. What he wanted was to continue down on the floor and disappear into a dark corner until everything settled.

He heard the door close. When the chair beside his moved, he looked up. Peter and he were alone in the conference room.

"I don't deserve this" Neal had never been surer of anything in his life. Minutes ago he was about to confess to a crime that would put him away in prison for a long time. Now someone thought he was possibly worthy of his freedom.

"You have done a great job for the FBI" Peter pointed out.

"What happens now, Peter? Where does this leave us?"

"We continue the work as usual."

"I meant with us. Are we still friends?"

Peter watched him in silence. Neal wanted to scream, to beg, do anything to get Peter's friendship back.

"Neal... I am your friend. But you said you never lied to me, and until the day before yesterday, I did believe you on that point. I can't any longer." Neal nodded.

"I don't blame you." That treasure had meant nothing but bad luck for him. He wished that Mozzie never stole it but must of all he wished that he had walked away, let Mozzie have it all. But he had not, and regrets were of little use. Time moved forward, and it was nothing he could do about it.

"You need to understand that what you do get consequences not only for yourself. It affects your family too. Me and El. I can accept that you think something is worth a risk to get to prison. But you must get into your head that it's not only you who is affected. Not any longer."

"I do understand that now." Neal was ashamed for not consider it before. Peter and Elisabeth and Sara, they were all people for others to use. He ought to feel trapped, but he did not. He just felt like a reckless schoolboy.

"Do you?" Peter leaned forward. "I appreciate that you were ready to confess, truly, I do. But this is not just about you, and me being disappointed."

No, it was not. But Neal, on the other hand, had taken care of himself since he was a boy. He had never learned to consider other people. Yet a lesson to be learned this day.

"Can I see Elisabeth?" he asked.

"What for?"

"For the reasons you just said. To say I'm sorry." Peter nodded and sent him a smile.

"Come by for dinner."

"No. No, I can't."

"Yes, you can. And Neal?"

"Yeah?"

"You came here this morning believing you would go to prison. Take the day off. Find your footing again." Neal rose with an effort that seemed inhumane.

"Thanks, Peter. Truly."

"See you tonight."

"Yeah."

* * *

When Elisabeth let him in he held a bottle of fine wine in his hands.

"I know this will never replace..." For once Neal did not find the words. Elisabeth smiled, accepted the bottle and pulled him into the kitchen.

"Peter is out on an errand" she informed him. "I think he intended to let us talk without ears." Neal saw Elisabeth was watching him.

"El, I... I've caused a lot of trouble for you both the past two years... and you've always been there with your open arms, no matter what. And... I know nothing I do will ever fully heal the damage I caused."

Elisabeth placed the wine bottle on the counter. She stood with her back to him, and he wished he could read her expression. She turned, stern.

"Neal, you lied to Peter."

"I did." It was no use trying to find a loophole out of it. He had had every intention not to tell Peter. Even if it meant he had to lie.

"Why didn't you just walk away from the treasure?"

"You know why. I'm a con-man, a thief. That's what I've been since I was a kid. And El, I have never had to care for anybody but myself. Those around me were the same. No one has ever been there for me as you have. I didn't have a clue what the treasure would lead to. I knew I risked being thrown back into prison, but I could not see this coming. Neither did Mozzie. If he had, he would've kept me out of it. None of us would ever want to harm any of you."

Elisabeth nods.

"I know. I just... Neal, I hated when we couldn't trust each other. When I didn't know if you came to visit _me_ or had an angle to it. Peter was so sure you had stolen it and... You may not have been lying, but you didn't tell him the truth either. You deceived him. Or tried to."

Neal nods.

"If you had told him," Elisabeth continued, "you would've gone to prison. But you would have had Peter's trust. I knew you've been working very hard to make him trust you."

"But he never did," Neal mumbled and bit his tongue.

"What?"

"El, don't get me wrong but before the treasure, I had never given Peter reason _not_ to trust me. When he accused me that day, at the fire, I was so mad at him. I had done everything to prove myself, to show he could trust me. And yet he threw that accusation into my face. When I then learned what happened and faced the treasure, I felt that whatever I did, Peter would never trust me anyway. Why waste this chance of a lifetime?"

"Do you blame Peter for this?" Elisabeth frowned.

"No! I explain why I didn't just walk away." Neal sighed. "And why I never told Peter when I should've. Whatever I did, Peter saw nothing but a con-man in me. If he couldn't see me as honest... I had tried everything, El. I was disappointed, angry. And tired of trying." Nothing had ever hurt that much as when Peter accused him. When he had done everything he could to do the right thing, to get Peter's trust, but it had not been enough. Peter had still been nothing but a criminal.

Elisabeth hugged him.

"Thank you. For being honest and telling me."

"Thank you" Neal hugs her back. "You're the only family I've got."

Peter opened the front door. He smiled when he saw them.

"Hon" Elisabeth greeted him. "I think Neal has something he would like to tell you about trust." Neal felt he could not breathe. "Relax, Neal" El assured him. "Just tell him what you told me."

* * *

Peter could not sleep that night.

Neal had explained how he had seen the situation when he came across the treasure. He had admitted that he should have walked away and let Mozzie have it. But the reason that he had not had been Peter's doing.

Peter had never trusted Neal not doing illegal things when he felt the need to, and on that point, Peter thought it was justified. But had he ever showed Neal how much he trusted him in doing his job? How many times had he told the kid that he saw hope, that he trusted him in so many ways, compared to all the times he had shown him nothing but suspicion, often about things not related to the job. Had he missed giving the kid feedback on the good stuff?

He had believed Neal stole the treasure and he had thrown it at his face at a time things could have gone otherwise if he had not. Peter wondered what would have happened if he had stopped by and talked to Neal and told him he was sorry the next day, instead of starting a hunt for evidence. Neal had deceived him, but not before Peter had shown him the ultimate distrust. He had to learn to live with that mistake.


	4. Message about novels

Please read my fan fiction novel on this site for more missing scenes, but in a context.

I have up to this date three finished novels and started a fouths. Part 5 will end season one. Thank you kindly for all your support.


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